I have found the solution after a bit of digging around.
For some reason, it is considering itself something other than 
XDG_CURRENT_DESKTOP - hence trying to invoke gnome-desktop-item-edit.
However, it is a command related to gnome-panel. So I changed the command to 
exo-desktop-item-edit like this:

if os.getenv("XDG_CURRENT_DESKTOP") == "XFCE":
            process = subprocess.Popen(['exo-desktop-item-edit', file_path], 
env=os.environ)
        else:
            process = subprocess.Popen(['exo-desktop-item-edit', file_path], 
env=os.environ)
        GObject.timeout_add(100, self.waitForNewMenuProcess, process, 
parent.get_menu_id(), file_path)

This is to be done for both new menu and new item function. The file is
at

/usr/share/alacarte/Alacarte/MainWindow.py

And everything started working in alacarte. I have also attached the
changed MainWindow.py file as a patch with this post.

Thank you.

** Attachment added: "Patched MainWindow.py file for Alacarte."
   
https://bugs.launchpad.net/ubuntu/+source/alacarte/+bug/1089438/+attachment/3460911/+files/MainWindow.py

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https://bugs.launchpad.net/bugs/1089438

Title:
  alacarte menu editor: new item, new menu bug

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